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Gene Sleuthing

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Gene Sleuthing Lorraine Sartori Majid Masso Paul R. McCreary Objectives: Search a data base to find a colon cancer gene Obtain information about the gene Use ... – PowerPoint PPT presentation

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Title: Gene Sleuthing


1
Gene Sleuthing
  • Lorraine Sartori
  • Majid Masso
  • Paul R. McCreary

2
Objectives
  • Search a data base to find a colon cancer gene
  • Obtain information about the gene
  • Use Biology Workbench to find the expressed
    genes protein sequence
  • Determine the structure of the protein
  • Use microarray to locate the normal gene

3
Search For a Colon Cancer Gene
  1. Go to http//bioquest.org/bedrock/
  2. Click on resources and then Other Resources
  3. Click on OMIM
  4. Search for colon cancer
  5. Select 114500

4
Obtain Information about the gene
5


                                                                    
  • Growth factor-induced protein phosphorylation
    plays a key role in the signal transduction that
    leads to mitogenic responses. Most growth factor
    receptors are transmembrane tyrosine kinases or
    are associated with cytoplasmic tyrosine kinases.
    However, another class of transmembrane receptors
    is predicted to function as serine-threonine
    kinases. The type II activin receptor (102581)
    and the types I (190181) and II TGF-beta
    receptors (Lin et al., 1992) belong to the
    serine-threonine kinase family. The many
    activities of TGF-beta in regulating cell
    proliferation and differentiation and
    extracellular matrix production are mediated
    through these receptors. With the use of cells
    overexpressing truncated type II receptors as
    dominant-negative mutants to block type II
    receptor signaling selectively, Chen et al.
    (1993) demonstrated the existence of 2 receptor
    pathways. The type II receptors, possibly in
    conjunction with type I receptors, mediate the
    induction of growth inhibition and
    hypophosphorylation of the retinoblastoma gene
    product. The type I receptors are responsible for
    effects on extracellular matrix, such as the
    induction of fibronectin and plasminogen
    activator inhibitor I, and for increased JUNB
    (165161) expression. Selective inactivation of
    the type II receptors alters the response to
    TGF-beta in a manner similar to the functional
    inactivation of the RB protein, suggesting a role
    for RB in the type II, but not the type I,
    receptor pathway.

6
Biology Workbench
  • Use Biology Workbench to find the expressed
    genes protein sequence
  • Go to http//bioquest.org/bedrock/
  • Click on resources and then Other Resources
  • Click on Biology Workbench
  • Log in

7
Choose Protein
  • Choose Ndjinn
  • Search for colon cancer gene 1ktz
  • Choose the pdb finder
  • Search for tgf beta type II receptor
  • Import the Protein Sequence
  • Use Swiss PDB Viewer to study Protein Structure

8
PDB ID 1KTZTransforming Growth Factor II
Receptor
9
Use microarray to locate the normal gene
  • You have been given a microarray chip with spots
    of normal human DNA restriction fragments from
    chromosome 3
  • You have Cy3 labeled (green) normal cDNA
  • You have Cy5 labeled (red) cDNA from the tumor
    cells
  • You flood the microarray with the sample mixture
    containing both labeled cDNAs
  • View the chip

10
Microarray Data Visualization
11
What do your detective skills tell you?
12
Future Work
  • DNA
  • Isolate the fragment from the DNA chip
  • Sequence the fragment
  • Look for similar fragments in other organisms
  • Do multiple alignments
  • Determine relatedness

13
Future Work
  • Protein
  • Look for similar protein sequences
  • Do multiple sequence alignments
  • Determine relatedness
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